ASDC_DNA {ftrCOOL}

Adaptive skip dinucleotide composition_DNA) (ASDC_DNA)

Description

This descriptor sufficiently considers the correlation information present not only between adjacent nucleotides but also between intervening nucleotides This function calculates frequency of pair nucleotides omitting gaps between them. Then this function normalizes each value through dividing each frequency by summition(frequencies).

Usage

ASDC_DNA(seqs, ORF = FALSE, reverseORF = TRUE, label = c())

Arguments

seqs

is a FASTA file containing nucleotide sequences. The sequences start with '>'. Also, seqs could be a string vector. Each element of the vector is a nucleotide sequence.

ORF

(Open Reading Frame) is a logical parameter. If it is set to true, ORF region of each sequence is considered instead of the original sequence (i.e., 3-frame).

reverseORF

is a logical parameter. It is enabled only if ORF is true. If reverseORF is true, ORF region will be searched in the sequence and also in the reverse complement of the sequence (i.e., 6-frame).

label

is an optional parameter. It is a vector whose length is equivalent to the number of sequences. It shows the class of each entry (i.e., sequence).

Value

The function returns a feature matrix. The number of rows is equal to the number of sequences and the number of columns is 16 (All posible nucleotide pairs).

References

Wei L, Zhou C, Chen H, Song J, Su R. ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides. Bioinformatics (2018).

Examples

fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
fileLNC<-fa.read(file=fileLNC,alphabet="dna")[1:5]
mat1<-ASDC_DNA(seqs=fileLNC,ORF=TRUE,reverseORF=FALSE)